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| | ==Rap1/DNA complex== | | ==Rap1/DNA complex== |
| - | <StructureSection load='4gfb' size='340' side='right' caption='[[4gfb]], [[Resolution|resolution]] 2.99Å' scene=''> | + | <StructureSection load='4gfb' size='340' side='right'caption='[[4gfb]], [[Resolution|resolution]] 2.99Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4gfb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GFB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GFB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4gfb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GFB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GFB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ukg|3ukg]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4gfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gfb OCA], [https://pdbe.org/4gfb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gfb RCSB], [https://www.ebi.ac.uk/pdbsum/4gfb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gfb ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RAP1, GRF1, TUF1, YNL216W, N1310 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4gfb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gfb OCA], [http://pdbe.org/4gfb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gfb RCSB], [http://www.ebi.ac.uk/pdbsum/4gfb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gfb ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RAP1_YEAST RAP1_YEAST]] Essential regulatory protein in yeast whose DNA-binding sites are found at three types of chromosomal elements: promoters, silencers, and telomeres. RAP1 is also involved in the regulation of telomere structure, where its binding sites are found within the terminal poly[C(1-3)A] sequences. The opposite regulatory functions of RAP1 are not intrinsic to its binding sites but, instead, result from interactions with different factors at promoters and silencers. RAP1 associates with SIR3 and SIR4 proteins to form a DNA-binding complex that initiates the repression at the HM loci and telomeres. May also target the binding of RIF1 and RIF2 to silencers and telomeres. Forms with GCR1 a transcriptional activation complex that is required for expression of glycolytic and ribosomal gene. | + | [https://www.uniprot.org/uniprot/RAP1_YEAST RAP1_YEAST] Essential regulatory protein in yeast whose DNA-binding sites are found at three types of chromosomal elements: promoters, silencers, and telomeres. RAP1 is also involved in the regulation of telomere structure, where its binding sites are found within the terminal poly[C(1-3)A] sequences. The opposite regulatory functions of RAP1 are not intrinsic to its binding sites but, instead, result from interactions with different factors at promoters and silencers. RAP1 associates with SIR3 and SIR4 proteins to form a DNA-binding complex that initiates the repression at the HM loci and telomeres. May also target the binding of RIF1 and RIF2 to silencers and telomeres. Forms with GCR1 a transcriptional activation complex that is required for expression of glycolytic and ribosomal gene. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | + | [[Category: Large Structures]] |
| - | [[Category: Bihan, Y V.Le]] | + | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Du, M H.Le]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Matot, B]] | + | [[Category: Le Bihan Y-V]] |
| - | [[Category: Double-myb]] | + | [[Category: Le Du M-H]] |
| - | [[Category: Transcription-dna complex]] | + | [[Category: Matot B]] |
| Structural highlights
Function
RAP1_YEAST Essential regulatory protein in yeast whose DNA-binding sites are found at three types of chromosomal elements: promoters, silencers, and telomeres. RAP1 is also involved in the regulation of telomere structure, where its binding sites are found within the terminal poly[C(1-3)A] sequences. The opposite regulatory functions of RAP1 are not intrinsic to its binding sites but, instead, result from interactions with different factors at promoters and silencers. RAP1 associates with SIR3 and SIR4 proteins to form a DNA-binding complex that initiates the repression at the HM loci and telomeres. May also target the binding of RIF1 and RIF2 to silencers and telomeres. Forms with GCR1 a transcriptional activation complex that is required for expression of glycolytic and ribosomal gene.
Publication Abstract from PubMed
Repressor activator protein 1 (Rap1) is an essential factor involved in transcription and telomere stability in the budding yeast Saccharomyces cerevisiae. Its interaction with DNA causes hypersensitivity to potassium permanganate, suggesting local DNA melting and/or distortion. In this study, various Rap1-DNA crystal forms were obtained using specifically designed crystal screens. Analysis of the DNA conformation showed that its distortion was not sufficient to explain the permanganate reactivity. However, anomalous data collected at the Mn edge using a Rap1-DNA crystal soaked in potassium permanganate solution indicated that the DNA conformation in the crystal was compatible with interaction with permanganate ions. Sequence-conservation analysis revealed that double-Myb-containing Rap1 proteins all carry a fully conserved Arg580 at a position that may favour interaction with permanganate ions, although it is not involved in the hypersensitive cytosine distortion. Permanganate reactivity assays with wild-type Rap1 and the Rap1[R580A] mutant demonstrated that Arg580 is essential for hypersensitivity. AFM experiments showed that wild-type Rap1 and the Rap1[R580A] mutant interact with DNA over 16 successive binding sites, leading to local DNA stiffening but not to accumulation of the observed local distortion. Therefore, Rap1 may cause permanganate hypersensitivity of DNA by forming a pocket between the reactive cytosine and Arg580, driving the permanganate ion towards the C5-C6 bond of the cytosine.
Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity.,Le Bihan YV, Matot B, Pietrement O, Giraud-Panis MJ, Gasparini S, Le Cam E, Gilson E, Sclavi B, Miron S, Le Du MH Acta Crystallogr D Biol Crystallogr. 2013 Mar;69(Pt 3):409-19. doi:, 10.1107/S0907444912049311. Epub 2013 Feb 16. PMID:23519416[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Le Bihan YV, Matot B, Pietrement O, Giraud-Panis MJ, Gasparini S, Le Cam E, Gilson E, Sclavi B, Miron S, Le Du MH. Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity. Acta Crystallogr D Biol Crystallogr. 2013 Mar;69(Pt 3):409-19. doi:, 10.1107/S0907444912049311. Epub 2013 Feb 16. PMID:23519416 doi:http://dx.doi.org/10.1107/S0907444912049311
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